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Items: 1 to 20 of 62

1.

Measuring transcription factor-binding site turnover: a maximum likelihood approach using phylogenies.

Otto W, Stadler PF, López-Giraldéz F, Townsend JP, Lynch VJ, Wagner GP.

Genome Biol Evol. 2009 May 25;1:85-98. doi: 10.1093/gbe/evp010.

2.

A stochastic model for the evolution of transcription factor binding site abundance.

Wagner GP, Otto W, Lynch V, Stadler PF.

J Theor Biol. 2007 Aug 7;247(3):544-53. Epub 2007 Mar 7.

PMID:
17475285
4.

Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites.

Blanchette M.

BMC Bioinformatics. 2012;13 Suppl 19:S2. doi: 10.1186/1471-2105-13-S19-S2. Epub 2012 Dec 19.

5.

Incorporating evolution of transcription factor binding sites into annotated alignments.

Bais AS, Grossmann S, Vingron M.

J Biosci. 2007 Aug;32(5):841-50.

6.

Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.

He X, Ling X, Sinha S.

PLoS Comput Biol. 2009 Mar;5(3):e1000299. doi: 10.1371/journal.pcbi.1000299. Epub 2009 Mar 13.

7.

Regulatory motif finding by logic regression.

Keles S, van der Laan MJ, Vulpe C.

Bioinformatics. 2004 Nov 1;20(16):2799-811. Epub 2004 May 27.

PMID:
15166027
8.

A comparative analysis of relative occurrence of transcription factor binding sites in vertebrate genomes and gene promoter areas.

Stepanova M, Tiazhelova T, Skoblov M, Baranova A.

Bioinformatics. 2005 May 1;21(9):1789-96. Epub 2005 Feb 4.

PMID:
15699025
10.

Surveying phylogenetic footprints in large gene clusters: applications to Hox cluster duplications.

Prohaska SJ, Fried C, Flamm C, Wagner GP, Stadler PF.

Mol Phylogenet Evol. 2004 May;31(2):581-604.

PMID:
15062796
11.

Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA.

Pierstorff N, Bergman CM, Wiehe T.

Bioinformatics. 2006 Dec 1;22(23):2858-64. Epub 2006 Oct 10.

PMID:
17032682
12.
13.

Favorable genomic environments for cis-regulatory evolution: A novel theoretical framework.

Maeso I, Tena JJ.

Semin Cell Dev Biol. 2016 Sep;57:2-10. doi: 10.1016/j.semcdb.2015.12.003. Epub 2015 Dec 8. Review.

PMID:
26673387
14.

Evolution of motif variants and positional bias of the cyclic-AMP response element.

Smith B, Fang H, Pan Y, Walker PR, Famili AF, Sikorska M.

BMC Evol Biol. 2007 Feb 8;7 Suppl 1:S15.

15.

ReAlignerV: web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences.

Iwama H, Hori Y, Matsumoto K, Murao K, Ishida T.

BMC Bioinformatics. 2008 Feb 22;9:112. doi: 10.1186/1471-2105-9-112.

16.

Detection and visualization of compositionally similar cis-regulatory element clusters in orthologous and coordinately controlled genes.

Jegga AG, Sherwood SP, Carman JW, Pinski AT, Phillips JL, Pestian JP, Aronow BJ.

Genome Res. 2002 Sep;12(9):1408-17.

17.

Evolution of cis-acting elements in 5' flanking regions of vertebrate actin genes.

Liu T, Wu J, He F.

J Mol Evol. 2000 Jan;50(1):22-30.

PMID:
10654256
18.
19.

rVISTA 2.0: evolutionary analysis of transcription factor binding sites.

Loots GG, Ovcharenko I.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W217-21.

20.

Molecular evolution of the HoxA cluster in the three major gnathostome lineages.

Chiu CH, Amemiya C, Dewar K, Kim CB, Ruddle FH, Wagner GP.

Proc Natl Acad Sci U S A. 2002 Apr 16;99(8):5492-7. Epub 2002 Apr 9.

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